I think you just need to match the midi channel for upper manual. Midi organ modules and even Organ VST instruments ususally take 3 different midi channels; the upper, the lower, and the pedal.

Just found this in the manual page 2

Attach your MIDI keyboard to MIDI A. You can play the
upper register (manual) via MIDI channel 1. The lower register
is on MIDI channel 2, and the pedal register on MIDI channel
3. In order to attach another MIDI keyboard for the lower
register easily, use the MIDI B input. Here channel 1 is set to
the lower register.
To load a preset, press the Preset key, and select the desired
preset with knob A.